Input and runtime details for job 6860187 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
62	0.006126	0.3261	b3824	rhtB	-10.68	0.204362	7 -- 23	171 -- 187	homoserine homoserine lactone and S-methyl-methionine efflux pump	_____________6_________________24\n_____________\|_________________\|\n_____5'-ACGCUG_______AAA_______GCGGU...ACC-3'\n______________ACGCCAG___UCAGUCA\n______________\|\|:\|\|\|:___\|\|\|\|\|\|\|\n______________UGUGGUU___AGUCAGU\n3'-UUU...UAAAA_______AUG_______GUGUA...UAG-5'\n_____________\|_________________\|\n_____________188_______________170\n	17 -- 23	171 -- 177	-18.1223 kcal/mol	1.9449 kcal/mol	4.7016 kcal/mol	6 24@LB@ \| \|@LB@ 5'-ACGCUG AAA GCGGU...ACC-3'@LB@ ACGCCAG UCAGUCA@LB@ \|\|:\|\|\|: \|\|\|\|\|\|\|@LB@ UGUGGUU AGUCAGU@LB@3'-UUU...UAAAA AUG GUGUA...UAG-5'@LB@ \| \|@LB@ 188 170@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -18.1223 kcal/mol@LB@Unfolding Energy - mRNA 1.9449 kcal/mol@LB@Unfolding Energy - sRNA 4.7016 kcal/mol@LB@@LB@Position - mRNA 7 -- 23@LB@Position - sRNA 171 -- 187@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 171 -- 177@LB@
194	0.02283	0.3833	b3823	rhtC	-9.67	0.316154	216 -- 300	113 -- 178	threonine efflux pump	_____________215___________________301\n_____________\|_____________________\|\n5'-AGA...UAUUU____CC_______________CAUUG...GUU-3'\n______________CUCA__GUCGC_CAUGGUGCA\n______________\|\|\|\|__\|\|\|:\|_\|\|\|\|:\|\|\|\|\n______________GAGU__CAGUG_GUACUACGU\n3'-UUU...GUUAU___________U_________CCGUU...UAG-5'\n_____________\|_____________________\|\n_____________179___________________112\n	228 -- 234	161 -- 167	-23.3741 kcal/mol	7.13181 kcal/mol	4.79874 kcal/mol	215 301@LB@ \| \|@LB@5'-AGA...UAUUU CC CAUUG...GUU-3'@LB@ CUCA GUCGC CAUGGUGCA@LB@ \|\|\|\| \|\|\|:\| \|\|\|\|:\|\|\|\|@LB@ GAGU CAGUG GUACUACGU@LB@3'-UUU...GUUAU U CCGUU...UAG-5'@LB@ \| \|@LB@ 179 112@LB@@LB@@LB@Energy -9.67 kcal/mol@LB@Hybridization Energy -23.3741 kcal/mol@LB@Unfolding Energy - mRNA 7.13181 kcal/mol@LB@Unfolding Energy - sRNA 4.79874 kcal/mol@LB@@LB@Position - mRNA 216 -- 300@LB@Position - sRNA 113 -- 178@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 161 -- 167@LB@
49	0.004667	0.3205	b1277	ribA	-9.86	0.291903	241 -- 249	16 -- 24	GTP cyclohydrolase II	_____________240________250\n_____________\|__________\|\n5'-CCA...AAUAC__________UUAUC...UCG-3'\n______________AGAACCAGCA\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUUGGUCGU\n_______3'-UUUU__________CCAUA...UAG-5'\n_____________\|__________\|\n_____________25_________15\n	178 -- 184	214 -- 220	-13.9783 kcal/mol	2.87719 kcal/mol	5.75438 kcal/mol	240 250@LB@ \| \|@LB@5'-CCA...AAUAC UUAUC...UCG-3'@LB@ AGAACCAGCA@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUUGGUCGU@LB@ 3'-UUUU CCAUA...UAG-5'@LB@ \| \|@LB@ 25 15@LB@@LB@@LB@Energy -9.86 kcal/mol@LB@Hybridization Energy -13.9783 kcal/mol@LB@Unfolding Energy - mRNA 2.87719 kcal/mol@LB@Unfolding Energy - sRNA 5.75438 kcal/mol@LB@@LB@Position - mRNA 241 -- 249@LB@Position - sRNA 16 -- 24@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 214 -- 220@LB@
148	0.01584	0.3602	b1822	rlmA	-10.68	0.203557	148 -- 239	111 -- 186	23S rRNA m(1)G745 methyltransferase SAM-dependent	_____________147___________240\n_____________\|_____________\|\n5'-AAG...GCGUG_____C_______UUGCG...GGU-3'\n______________AUUCG_GUUACAC\n______________\|:\|\|:_\|\|:\|\|\|\|\n______________UGAGU_CAGUGUG\n3'-UUU...GGUUA_____________UACUA...UAG-5'\n_____________\|_____________\|\n_____________187___________110\n	163 -- 169	168 -- 174	-12.5288 kcal/mol	1.89227 kcal/mol	0.283892 kcal/mol	147 240@LB@ \| \|@LB@5'-AAG...GCGUG C UUGCG...GGU-3'@LB@ AUUCG GUUACAC@LB@ \|:\|\|: \|\|:\|\|\|\|@LB@ UGAGU CAGUGUG@LB@3'-UUU...GGUUA UACUA...UAG-5'@LB@ \| \|@LB@ 187 110@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -12.5288 kcal/mol@LB@Unfolding Energy - mRNA 1.89227 kcal/mol@LB@Unfolding Energy - sRNA 0.283892 kcal/mol@LB@@LB@Position - mRNA 148 -- 239@LB@Position - sRNA 111 -- 186@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 168 -- 174@LB@
16	0.0008966	0.1886	b0807	rlmF	-16.29	0.014793	117 -- 160	51 -- 97	23S rRNA m(6)A1618 methyltransferase SAM-dependent	_____________116_____________________________________________161\n_____________\|_______________________________________________\|\n5'-AUU...UUAAG___U_____AA______A_______________U__A_C________UUAUG...UCC-3'\n______________GUU_UGGGG____UGAU_AACGCAGCCAG_AUA_UU_C_CUGUCGCG\n______________\|\|\|_\|\|\|\|:____\|:\|:_\|\|\|\|\|\|:\|\|\|\|_\|:\|_:\|_\|_\|\|\|\|\|\|\|\|\n______________CAA_ACCCU____AUUG_UUGCGUUGGUC_UGU_GA_G_GACAGCGC\n3'-UUU...AUUAG___C_____GCGA____G___________G___U__A_C________CAUUU...UAG-5'\n_____________\|_______________________________________________\|\n_____________98______________________________________________50\n	154 -- 160	51 -- 57	-44.7843 kcal/mol	10.0752 kcal/mol	25.3667 kcal/mol	116 161@LB@ \| \|@LB@5'-AUU...UUAAG U AA A U A C UUAUG...UCC-3'@LB@ GUU UGGGG UGAU AACGCAGCCAG AUA UU C CUGUCGCG@LB@ \|\|\| \|\|\|\|: \|:\|: \|\|\|\|\|\|:\|\|\|\| \|:\| :\| \| \|\|\|\|\|\|\|\|@LB@ CAA ACCCU AUUG UUGCGUUGGUC UGU GA G GACAGCGC@LB@3'-UUU...AUUAG C GCGA G G U A C CAUUU...UAG-5'@LB@ \| \|@LB@ 98 50@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -44.7843 kcal/mol@LB@Unfolding Energy - mRNA 10.0752 kcal/mol@LB@Unfolding Energy - sRNA 25.3667 kcal/mol@LB@@LB@Position - mRNA 117 -- 160@LB@Position - sRNA 51 -- 97@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 51 -- 57@LB@
44	0.003817	0.292	b0967	rlmI	-10.41	0.230051	81 -- 118	128 -- 161	23S rRNA m(5)C1962 methyltransferase SAM-dependent	_____________80_________________________________119\n_____________\|__________________________________\|\n5'-CGU...UGAAC____C___AAACC_______UUAU_CA_______GACAU...AAG-3'\n______________UCGC_CGU_____CAGGCAA____G__GACUUUC\n______________\|\|:\|_\|:\|_____\|\|\|\|\|\|\|____\|__:\|\|\|\|\|\|\n______________AGUG_GUA_____GUCCGUU____C__UUGAAAG\n3'-UUU...GAGUC____U___CUAC_____________AG_______UCUUA...UAG-5'\n_____________\|__________________________________\|\n_____________162________________________________127\n	95 -- 101	145 -- 151	-21.0542 kcal/mol	5.99356 kcal/mol	7.97203 kcal/mol	80 119@LB@ \| \|@LB@5'-CGU...UGAAC C AAACC UUAU CA GACAU...AAG-3'@LB@ UCGC CGU CAGGCAA G GACUUUC@LB@ \|\|:\| \|:\| \|\|\|\|\|\|\| \| :\|\|\|\|\|\|@LB@ AGUG GUA GUCCGUU C UUGAAAG@LB@3'-UUU...GAGUC U CUAC AG UCUUA...UAG-5'@LB@ \| \|@LB@ 162 127@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.99356 kcal/mol@LB@Unfolding Energy - sRNA 7.97203 kcal/mol@LB@@LB@Position - mRNA 81 -- 118@LB@Position - sRNA 128 -- 161@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 145 -- 151@LB@
127	0.01385	0.3575	b3832	rmuC	-11.83	0.120260	236 -- 246	193 -- 203	DNA recombination protein	_____________235____________________________________________________________247\n_____________\|______________________________________________________________\|\n5'-AAA...UUGUA________AUUC___UUU_____________GUU__G______AGGC_______AUU_____AUCAU...AGC-3'\n______________CAG_CACA____UAU___GUGCGGGUAAGUU___GC__UCAGG____GUUGUGG___UCUCA\n______________\|\|\|_\|\|\|\|____:\|\|___:\|\|\|:\|\|:\|\|\|\|:___:\|__\|\|\|\|:____:\|\|\|:\|\|___\|\|:\|\|\n______________GUC_GUGU____GUA___UACGUCCGUUCAG___UG__AGUCU____UAACGCC___AGGGU\n3'-UUU...UAUGA___A___________C_______________U____AA________________AGU_____GACGU...UAG-5'\n_____________\|______________________________________________________________\|\n_____________204____________________________________________________________192\n	198 -- 204	135 -- 141	-42.9883 kcal/mol	19.1075 kcal/mol	15.6146 kcal/mol	235 247@LB@ \| \|@LB@5'-AAA...UUGUA AUUC UUU GUU G AGGC AUU AUCAU...AGC-3'@LB@ CAG CACA UAU GUGCGGGUAAGUU GC UCAGG GUUGUGG UCUCA@LB@ \|\|\| \|\|\|\| :\|\| :\|\|\|:\|\|:\|\|\|\|: :\| \|\|\|\|: :\|\|\|:\|\| \|\|:\|\|@LB@ GUC GUGU GUA UACGUCCGUUCAG UG AGUCU UAACGCC AGGGU@LB@3'-UUU...UAUGA A C U AA AGU GACGU...UAG-5'@LB@ \| \|@LB@ 204 192@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -42.9883 kcal/mol@LB@Unfolding Energy - mRNA 19.1075 kcal/mol@LB@Unfolding Energy - sRNA 15.6146 kcal/mol@LB@@LB@Position - mRNA 236 -- 246@LB@Position - sRNA 193 -- 203@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 135 -- 141@LB@
142	0.01524	0.3575	b0611	rna	-12.80	0.076457	138 -- 176	173 -- 202	ribonuclease I	_____________137_____________________________________177\n_____________\|_______________________________________\|\n5'-UAC...CCCAC________CUUUUUUA______A___GA___________GUAUG...AUU-3'\n______________CUGGCGGG________UGAUUU_AUA__UAGUAUUCAGU\n______________\|\|\|\|\|\|\|\|________\|\|\|\|\|\|_\|:\|__:\|:\|\|:\|\|\|\|\|\n______________GACCGCCC________ACUAAA_UGU__GUUAUGAGUCA\n3'-UUU...UAGAC______________________A___G____________GUGUG...UAG-5'\n_____________\|_______________________________________\|\n_____________203_____________________________________172\n	170 -- 176	173 -- 179	-31.7889 kcal/mol	9.30484 kcal/mol	14.6886 kcal/mol	137 177@LB@ \| \|@LB@5'-UAC...CCCAC CUUUUUUA A GA GUAUG...AUU-3'@LB@ CUGGCGGG UGAUUU AUA UAGUAUUCAGU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\| :\|:\|\|:\|\|\|\|\|@LB@ GACCGCCC ACUAAA UGU GUUAUGAGUCA@LB@3'-UUU...UAGAC A G GUGUG...UAG-5'@LB@ \| \|@LB@ 203 172@LB@@LB@@LB@Energy -12.80 kcal/mol@LB@Hybridization Energy -31.7889 kcal/mol@LB@Unfolding Energy - mRNA 9.30484 kcal/mol@LB@Unfolding Energy - sRNA 14.6886 kcal/mol@LB@@LB@Position - mRNA 138 -- 176@LB@Position - sRNA 173 -- 202@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 173 -- 179@LB@
26	0.002141	0.2633	b0183	rnhB	-16.17	0.015603	251 -- 292	123 -- 175	ribonuclease HII degrades RNA of DNA-RNA hybrids	______________251_______________________________________________________293\n______________\|_________________________________________________________\|\n___________5'-____________________________AG_G_______AAGAAUUAU__________AGUGU...UCC-3'\n______________AAUCUGCUGGCGGG___________CAG__A_UUAGUCA_________UGCAGG_AAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|___________\|\|:__\|_\|:\|\|\|\|\|_________\|\|\|\|\|\|_\|\|\|\n______________UUAGACGACCGCCC___________GUU__U_AGUCAGU_________ACGUCC_UUC\n3'-UUU...CCAUA______________ACUAAAAUGUG___A__G_______GUGUACU________G___AGUUG...UAG-5'\n_____________\|__________________________________________________________\|\n_____________176________________________________________________________122\n	22 -- 28	171 -- 177	-46.3072 kcal/mol	12.4456 kcal/mol	20.994 kcal/mol	251 293@LB@ \| \|@LB@ 5'- AG G AAGAAUUAU AGUGU...UCC-3'@LB@ AAUCUGCUGGCGGG CAG A UUAGUCA UGCAGG AAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\|: \| \|:\|\|\|\|\| \|\|\|\|\|\| \|\|\|@LB@ UUAGACGACCGCCC GUU U AGUCAGU ACGUCC UUC@LB@3'-UUU...CCAUA ACUAAAAUGUG A G GUGUACU G AGUUG...UAG-5'@LB@ \| \|@LB@ 176 122@LB@@LB@@LB@Energy -16.17 kcal/mol@LB@Hybridization Energy -46.3072 kcal/mol@LB@Unfolding Energy - mRNA 12.4456 kcal/mol@LB@Unfolding Energy - sRNA 20.994 kcal/mol@LB@@LB@Position - mRNA 251 -- 292@LB@Position - sRNA 123 -- 175@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 171 -- 177@LB@
112	0.01232	0.3575	b1540	rspR	-15.19	0.024761	13 -- 44	171 -- 202	transcriptional repressor for rspAB	_____________12_________________________________________________________45\n_____________\|__________________________________________________________\|\n5'-CAG...GCCGU__________UCA_______GCC______C___A____CAAUACCCUGGAA_______CGGUU...GCA-3'\n______________CUGGUGGGUG_____ACGCU___UGCUCA_GUC_AUAU_____________AUGAUGC\n______________\|\|\|\|:\|\|\|\|\|_____\|\|:\|:___\|:\|\|\|\|_\|\|\|_\|:\|:_____________\|\|\|\|\|\|\|\n______________GACCGCCCAC_____UGUGG___AUGAGU_CAG_UGUG_____________UACUACG\n3'-UUU...UAGAC__________UAAAA_____UU____________________________________UCCGU...UAG-5'\n_____________\|__________________________________________________________\|\n_____________203________________________________________________________170\n	62 -- 68	161 -- 167	-40.6001 kcal/mol	15.8189 kcal/mol	17.3482 kcal/mol	12 45@LB@ \| \|@LB@5'-CAG...GCCGU UCA GCC C A CAAUACCCUGGAA CGGUU...GCA-3'@LB@ CUGGUGGGUG ACGCU UGCUCA GUC AUAU AUGAUGC@LB@ \|\|\|\|:\|\|\|\|\| \|\|:\|: \|:\|\|\|\| \|\|\| \|:\|: \|\|\|\|\|\|\|@LB@ GACCGCCCAC UGUGG AUGAGU CAG UGUG UACUACG@LB@3'-UUU...UAGAC UAAAA UU UCCGU...UAG-5'@LB@ \| \|@LB@ 203 170@LB@@LB@@LB@Energy -15.19 kcal/mol@LB@Hybridization Energy -40.6001 kcal/mol@LB@Unfolding Energy - mRNA 15.8189 kcal/mol@LB@Unfolding Energy - sRNA 17.3482 kcal/mol@LB@@LB@Position - mRNA 13 -- 44@LB@Position - sRNA 171 -- 202@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 161 -- 167@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching